Are my migraines from braces?

A migraine is not just a "really bad headache" but a vascular event in the brain. Most of the time, when someone says they have a migraine, they really mean their head hurts. A lot.
If metal braces created a headache, Invisalign would too. The same pressure is applied, same desired outcome. I would not change anything, but I would discuss it with the treating Dr.

Some people prefer wearing Invisalign aligners over conventional braces and others feel the opposite. It is very common to feel some discomfort (possibly headaches) when spacers are placed. That does not mean that the braces are causing migraines.

If all of the permanent teeth are nearly fully erupted, you can most likely opt to use Invisalign instead of braces, but that will depend on an individual’s dental situation. Your orthodontist should be able to help you formulate a treatment plan that will suit your individual needs and desires.

Invisalign doesnt need to space out your sons teeth so that brackets can fit around them. Therefore no headaches!! We put attachments on the tooth and move them that way. It can be less painful the Invisalign route and easier for your son to tolerate. Also he will have better hygiene with I.align than conventional braces. They now have Teen Invisalign so you may want to look into that.

Spacers hurt. They hurt a lot. This pain can radiate up into your head and create a headache. Invisalign can cause the same discomfort in the beginning. Most likely, this pain will subside soon and his teeth will feel better. They may be a little tender when he has his wires tightened -- Ibuprofen will help a lot (if he can take it).